If only a single cylinder is not firing, initial possibility to consider and/or check since "...good spark and comprestion..." would be the carb; or more specifically presence / absence of fuel in the carb bowl and its ability to deliver fuel through the intake manifold to the combustion chamber.

A simple check would be to collect the fuel from the carb of the cylinder not firing through the drain hose (bottom of the bowl) and loosening the drain screw. Note the quantity and quality of fuel. Doing the same with the other 3 carbs would give you a reference.

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Related Questions:

Hi, Anonymous you need a wiring diagram to check the second lead there is one in the back of the service manual and the usual suspects are:
1. Fouled spark plugs.
2. Severely discharged or a damaged battery, should have 12.5 volts or better and be able to pass a load test if necessary.
3. Check battery terminals for damage or corrosion, check the battery cables at "BOTH" ends for loose, corroded, or broken connectors, "INSIDE" and outside the cable harness, perform connector wiggle test and check cables with an ohmmeter if necessary.
4. Loose connection at ignition coil or plug between ignition sensor and module.
5. Spark plug cables in bad condition, shorting / leaking, spark plug cable connections loose.
6. Faulty ignition coil or electronic control module or CDI box.
7. Faulty CKP, CMP, or BAS sensor.
8. Faulty ignition switch.
9. Tilt sensor needs a reset.
10. Security alarm failing to disarm needs reset
For more information about your issue and valuable "FREE" downloads that you will need please click on the links. Good luck and have a nice day.http://www.carlsalter.com/pdfs/Yamaha_virago_xv250s_1999_servico.pdfOEM parts for YamahaYAMAHA XVS250 Owner Manual

mcdevito75 here, If there is enough mileage on the engine you could totally loose all compression. Remove 1 of the spark plugs and crank the motor, if you hear a chaa rush of air comming out of that cylinder you have compression and need to check something else.